--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/msms_extractor.xml	Tue Oct 29 11:09:46 2019 -0400
@@ -0,0 +1,81 @@
+<tool id="msms_extractor" name="msms_extractor" version="1.0.0">
+  <description>Extract MS/MS scans from the mzML file(s) based on PSM report</description>
+  <requirements>
+      <requirement type="package" version="3_0_9992">proteowizard</requirement>
+      <requirement type="package" version="3.7.3">python</requirement>
+      <requirement type="package" version="4.1.2">pyteomics</requirement>
+      <requirement type="package" version="0.25.2">pandas</requirement>
+  </requirements>
+  <command detect_errors="aggressive"><![CDATA[python '$__tool_directory__/msms_extractor.py' '$spectrumfile' '$psmreportfile' '$output' ${spectrumfile.name.rsplit('.',1)[0]} '$removeretain.doremoveretain' '$removeretain.num_random_scans']]></command>
+  <inputs>
+    <param name="spectrumfile" type="data" format="mzml" label="Input mzML File"/>
+    <param name="psmreportfile" type="data" format="tabular" label="Input PSM Report File"/>
+    
+    <conditional name="removeretain">
+        <param name="doremoveretain" type="select" display="radio" label="Retain or Remove the MS/MS scans that were identified in PSM report">
+            <option value="remove" selected="True">Remove the scans reported in the PSM Report File</option>
+            <option value="retain">Retain the scans reported in the PSM Report File </option>
+        </param>
+        
+        <when value="remove">
+            <param name="num_random_scans" type="hidden" value="0" />
+        </when>
+        <when value="retain">
+            <param name="num_random_scans" type="integer" label="Add N random scans in addition to those in the list" value="0" optional="true" />
+        </when>
+      </conditional>
+      
+  </inputs>
+
+  <outputs>
+    <data format="mzml" name="output" label="${spectrumfile.name.rsplit('.',1)[0]}.mzml" />
+  </outputs>
+  
+  <tests>
+    <test>
+        <param name="spectrumfile" value="Mo_Tai_iTRAQ_f1.mzml"/>
+        <param name="psmreportfile" value="test_psmreport.tabular"/>
+        <conditional name="removeretain">
+            <param name="doremoveretain" value="retain"/>
+            <param name="num_random_scans" value="5"/>
+        </conditional>
+        <output name="output">
+            <assert_contents>
+                <has_text text="Mo_Tai_iTRAQ_f1" />
+            </assert_contents>
+        </output>
+    </test>
+  </tests>
+
+  <help>
+msms_extractor reads scan numbers from the PSM report (scan numbers with identified PSM) and gives option to create a new mzml file, either with those scans or without those scans.
+
+----
+
+REMOVE option:
+
+Creates a new mzml file with all the unidentified scans (removes those that are in the PSM report).
+
+
+RETAIN option:
+
+Creates a new mzml file with only those scans that is present in the PSM report. In addition to this, it also has an option to add N number of randomly selected scans to the output mzml file.
+
+----
+
+Please Note: This tool currently works only with PeptideShaker generated PSM report file.
+
+
+This tool uses msconvert from ProteoWizard: Chambers, M.C., MacLean, B., Burke, R., Amode, D., Ruderman, D.L., Neumann, S., Gatto, L., Fischer, B., Pratt, B., Egertson, J., Hoff, K., Kessner, D., Tasman, N., Shulman, N., Frewen, B., Baker, T.A., Brusniak, M.-Y., Paulse, C., Creasy, D., Flashner, L., Kani, K., Moulding, C., Seymour, S.L., Nuwaysir, L.M., Lefebvre, B., Kuhlmann, F., Roark, J., Rainer, P., Detlev, S., Hemenway, T., Huhmer, A., Langridge, J., Connolly, B., Chadick, T., Holly, K., Eckels, J., Deutsch, E.W., Moritz, R.L., Katz, J.E., Agus, D.B., MacCoss, M., Tabb, D.L. and Mallick, P. A cross-platform toolkit for mass spectrometry and proteomics. Nature Biotechnology 30, 918-920 (2012).
+
+  </help>
+    <citations>
+        <citation type="bibtex">
+@misc{A cross-platform toolkit for mass spectrometry and proteomics,
+    author={Matt Chambers et al.},
+    year={2012},
+    title={ProteoWizard}
+}
+        </citation>
+    </citations>
+</tool>